scholarly journals Aspartate and asparagine tRNA genes in wheat mitochondrial DNA: a cautionary note on the isolation of tRNA genes from plants

1989 ◽  
Vol 17 (19) ◽  
pp. 7865-7878 ◽  
Author(s):  
Paul B. M. Joyce ◽  
Michael W. Gray
Keyword(s):  
Mitochondrial Dna ◽  
Trna Genes ◽  
Cautionary Note

Characterization of mutant mitochondrial plasmids of Neurospora spp. that have incorporated tRNAs by reverse transcription

1989 ◽  
Vol 9 (2) ◽  
pp. 678-691
Author(s):  
R A Akins ◽  
R L Kelley ◽  
A M Lambowitz
Keyword(s):  
Mitochondrial Dna ◽  
Reverse Transcription ◽  
Transcription Initiation ◽  
Consensus Sequence ◽  
Trna Genes ◽  
Wild Type ◽  
Mitochondrial Trna ◽  
Mitochondrial Plasmids ◽  
Circular Dnas ◽  
Mitochondrial Introns

The Mauriceville and Varkud mitochondrial plasmids of Neurospora spp. are closely related, closed-circular DNAs (3.6 and 3.7 kilobases, respectively) whose nucleotide sequences and genetic organization suggest relationships to mitochondrial introns and retroelements. We have characterized nine suppressive mutants of these plasmids that outcompete mitochondrial DNA and lead to impaired growth. All nine suppressive plasmids contain small insertions, corresponding to or including a mitochondrial tRNA (tRNATrp, tRNAGly, or tRNAVal) or a tRNA-like sequence. The insertions are located at the position corresponding to the 5' end of the major plasmid transcript or 24 nucleotides downstream near a cognate of the sequence at the major 5' RNA end. The structure of the suppressive plasmids suggests that the tRNAs were inserted via an RNA intermediate. The 3' end of the wild-type plasmid transcript can itself be folded into a secondary structure which has tRNA-like characteristics, similar to the tRNA-like structures at the 3' ends of plant viral RNAs. This structure may play a role in replication of the plasmids by reverse transcription. Major transcripts of the suppressive plasmids begin at the 5' end of the inserted mitochondrial tRNA sequence and are present in 25- to 100-fold-higher concentrations than are transcripts of wild-type plasmids. Mapping of 5' RNA ends within the inserted mtDNA sequences identifies a short consensus sequence (PuNPuAG) which is present at the 5' ends of a subset of mitochondrial tRNA genes. This sequence, together with sequences immediately upstream in the plasmids, forms a longer consensus sequence, which is similar to sequences at transcription initiation sites in Neurospora mitochondrial DNA. The suppressive behavior of the plasmids is likely to be directly related to the insertion of tRNAs leading to overproduction of plasmid transcripts.

A cautionary note on switching mitochondrial DNA reference sequences in forensic genetics

2012 ◽  
Vol 6 (6) ◽  
pp. e182-e184 ◽  
Author(s):  
Antonio Salas ◽  
Michael Coble ◽  
Stijn Desmyter ◽  
Tomasz Grzybowski ◽  
Leonor Gusmão ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Forensic Genetics ◽  
Cautionary Note ◽  
Reference Sequences

Yeast mitochondrial DNA specifies tRNA for 19 amino acids. Deletion mapping of the tRNA genes

Biochemistry ◽  
1977 ◽  
Vol 16 (21) ◽  
pp. 4672-4677 ◽  
Author(s):  
Nancy C. Martin ◽  
Murray Rabinowitz ◽  
Hiroshi Fukuhara
Keyword(s):  
Amino Acids ◽  
Mitochondrial Dna ◽  
Trna Genes ◽  
Deletion Mapping ◽  
Yeast Mitochondrial Dna

scholarly journals Characterization of tRNA genes in tRNA region II of yeast mitochondrial DNA

1980 ◽  
Vol 8 (21) ◽  
pp. 5007-5016 ◽  
Author(s):  
Dawn Newman ◽  
Hung D. Pham ◽  
Karen Underbrink-Lyon ◽  
Nancy C. Martin
Keyword(s):  
Mitochondrial Dna ◽  
Trna Genes ◽  
Region Ii ◽  
Yeast Mitochondrial Dna

The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA

Cell ◽  
1980 ◽  
Vol 22 (2) ◽  
pp. 393-403 ◽  
Author(s):  
Deanna Ojala ◽  
Christian Merkel ◽  
Robert Gelfand ◽  
Giuseppe Attardi
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Information ◽  
Trna Genes ◽  
Human Mitochondrial Dna

scholarly journals Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome of Daphnia Magna

2020 ◽  
Author(s):  
Krzysztof Kowal ◽  
Angelika Tkaczyk ◽  
Mariusz Pierzchała ◽  
Adam Bownik ◽  
Brygida Ślaska
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Daphnia Magna ◽  
Sequence Homology ◽  
Nuclear Genome ◽  
Complete Information ◽  
Trna Genes ◽  
Entire Genome ◽  
Mtdna Sequence ◽  
D Loop

Abstract Background: This is the first study in which the Daphnia magna (D. magna) nuclear genome deposited in the GenBank data-base was analyzed for pseudogene sequences of mitochondrial origin. The first complete information about the genome of D. magna was published by Lee et al. in 2019. To date, there is no information about pseudogenes localized in the genome of D. magna . The aim of the present study was to identify NUMTs, their length, homology, and location for potential use in evolutionary studies and to check whether their occurrence causes co-amplification during mitochondrial genome analyses.Results: Bioinformatic analysis showed 1909 fragments of the mitochondrial genome of D. magna , of which 1630 fragments were located in ten linkage groups (LG) of the nuclear genome (nDNA). The most frequently occurring fragments of the mtDNA sequence in the nuclear genome included ND2 (115), ND3 (113), and TRNA-CYS (110)). However, the highest number of NUMTs was observed for the D-loop (147). 253 fragments showed 100% homology (from 16 to 46 bp) with mtDNA gene sequences. The sequence homology for TRNA-MET was 100% for all 6 NUMTs (from 16 to 18 bp). The overall length of NUMTs in the nDNA was 44.391 bp (from 16 to 182 bp), which accounted for 0.042% of the entire genome.Conclusions: The best-matched NUMTs covering more than 90% of the mtDNA gene sequence have been identified for the TRNA-ARG (95%), TRNA-GLU (97%), and TRNA-THR (95%) genes, and they may be included in the functional nuclear tRNA genes. Using the product of total DNA isolation in mtDNA studies, coamplification of nDNA fragments is unlikely in the case of amplification of the whole tRNA genes as well as fragments of other genes and the D-loop with a length exceeding 200 bp. It was observed that TRNA-MET fragments had the highest level of sequence homology, which means that they could be evolutionarily the youngest. The lowest degree of homology was found in the pseudogene derived from the mtDNA D-loop sequence. It may probably be the oldest element of mitochondrial DNA incorporated into the nuclear genome; however, further analysis is necessary.

Frequent Mitochondrial DNA Mutations and Polymorphisms in Long-Term Survivors of Childhood Acute Lymphoblastic Leukemia.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2800-2800 ◽  
Author(s):  
Steven E. Lipshultz ◽  
Vernon E. Walker ◽  
Salina M. Torres ◽  
Dale M. Walker ◽  
Elly Barry ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Acute Lymphoblastic Leukemia ◽  
Myocardial Dysfunction ◽  
Lymphoblastic Leukemia ◽  
Negative Control ◽  
Trna Genes ◽  
Childhood All ◽  
Mtdna Mutations ◽  
Multi Agent

Abstract Progressive myocardial dysfunction, which can lead to cardiomyopathy, congestive heart failure, and sudden cardiac death, is a well-recognized late effect of several agents used in the treatment of childhood cancer. While the mechanism of this damage is not yet fully characterized, mounting data from rodent models implicate treatment-induced mitochondrial DNA (mtDNA) mutations as one potential mechanism of late cardiotoxicity. In the current study, the Dana-Farber Cancer Institute Acute Lymphoblastic Leukemia (ALL) Consortium collected peripheral blood mononuclear cell samples from 93 long-term ALL survivors who were 4 or more years post-doxorubicin and other multi-agent therapy including asparaginase, corticosteroids, vincristine, and methotrexate, as well as radiation therapy. Data from healthy newborn children (n=45) represented a negative control and data from children receiving highly active antiretroviral therapy (HAART) (mean age=11.3 years; SD=2.61; n=51) provided a positive control for mtDNA mutations. Maximum cumulative doxorubicin dose varied among patients by treatment protocol (median=300 mg/m2; range 45 mg/m2 to 470 mg/m2). Median age at treatment was 4.5 years (range=0.5 to 20.8 years) and at mtDNA screening, 14.9 years (range=6.0 to 41.1 years). The mitochondrial tRNA genes and flanking regions were screened via PCR-based denaturing gradient gel electrophoresis (DGGE). Preliminary data showed 47 confirmed polymorphisms or mutations in 39 of 93 ALL survivors screened (42%), occurring in PCR products from 6 of 13 primer sets. The mutation incidence in HIV positive controls receiving HAART was 35 changes in 25 of 51 patients (49%). To date, the negative control population data suggest the occurrence of very few to no polymorphisms or mutations. Most mtDNA changes in ALL survivors were distinct from those in children receiving HAART, and included some sequence variants with suggested pathogenic characteristics. Analysis of cardiac function is ongoing. These data suggest that childhood ALL and its treatment may lead to mutations, over-expression of rare polymorphisms, and the induction of persistent changes that when spontaneously occurring have been associated with clinically significant cardiac effects. Conclusive evidence that doxorubicin-containing multi-agent therapy leads to persistent mtDNA mutations fundamental to cardiac dysfunction might allow for the isolation and prevention of these cardiotoxic effects.

The Complete Mitochondrial Genomes of two Flying Fishes, Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii

2020 ◽  
Author(s):  
Liyan Qu ◽  
Heng Zhang ◽  
Fengying Zhang ◽  
Wei Wang ◽  
Fenghua Tang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Flying Fishes ◽  
Complete Mitochondrial Genomes

Background: Genome-scale approaches have played a significant role in the analysis of evolutionary relationships. Because of rich polymorphisms, high evolutionary rate and rare recombination, mitochondrial DNA sequences are commonly considered as effective markers for estimating population genetics, evolutionary and phylogenetic relationships. Flying fishes are important components of epipelagic ecosystems. Up to now, only few complete mitochondrial genomes of flying fishes have been reported. In the present study, the complete mitochondrial DNA sequences of the Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii had been determined. Methods: Based on the published mitogenome of Cheilopogon atrisignis (GenBank: KU360729), fifteen pairs of primers were designed by the software Primer Premier 5.0 to get the complete mitochondrial genomes of two flying fishes. According to the reported data, the phylogenetic position of two flying fishes were detected using the conserved 12 protein-coding genes. Result: The complete mitochondrial genomes of Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii are determined. They are 16532bp and 16525bp in length, respectively. And they both consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region. The OL regions are conserved in these two flying fishes and might have no function. From the tree topologies, we found C.p. japonicus and H. rondeletii clustered in a group. The findings of the study would contribute to the phylogenetic classification and the genetic conservation management of C.p. japonicus and H. rondeletii.

scholarly journals Characterization of mutant mitochondrial plasmids of Neurospora spp. that have incorporated tRNAs by reverse transcription.

1989 ◽  
Vol 9 (2) ◽  
pp. 678-691 ◽  
Author(s):  
R A Akins ◽  
R L Kelley ◽  
A M Lambowitz
Keyword(s):  
Mitochondrial Dna ◽  
Reverse Transcription ◽  
Transcription Initiation ◽  
Consensus Sequence ◽  
Trna Genes ◽  
Wild Type ◽  
Mitochondrial Trna ◽  
Mitochondrial Plasmids ◽  
Circular Dnas ◽  
Mitochondrial Introns

The Mauriceville and Varkud mitochondrial plasmids of Neurospora spp. are closely related, closed-circular DNAs (3.6 and 3.7 kilobases, respectively) whose nucleotide sequences and genetic organization suggest relationships to mitochondrial introns and retroelements. We have characterized nine suppressive mutants of these plasmids that outcompete mitochondrial DNA and lead to impaired growth. All nine suppressive plasmids contain small insertions, corresponding to or including a mitochondrial tRNA (tRNATrp, tRNAGly, or tRNAVal) or a tRNA-like sequence. The insertions are located at the position corresponding to the 5' end of the major plasmid transcript or 24 nucleotides downstream near a cognate of the sequence at the major 5' RNA end. The structure of the suppressive plasmids suggests that the tRNAs were inserted via an RNA intermediate. The 3' end of the wild-type plasmid transcript can itself be folded into a secondary structure which has tRNA-like characteristics, similar to the tRNA-like structures at the 3' ends of plant viral RNAs. This structure may play a role in replication of the plasmids by reverse transcription. Major transcripts of the suppressive plasmids begin at the 5' end of the inserted mitochondrial tRNA sequence and are present in 25- to 100-fold-higher concentrations than are transcripts of wild-type plasmids. Mapping of 5' RNA ends within the inserted mtDNA sequences identifies a short consensus sequence (PuNPuAG) which is present at the 5' ends of a subset of mitochondrial tRNA genes. This sequence, together with sequences immediately upstream in the plasmids, forms a longer consensus sequence, which is similar to sequences at transcription initiation sites in Neurospora mitochondrial DNA. The suppressive behavior of the plasmids is likely to be directly related to the insertion of tRNAs leading to overproduction of plasmid transcripts.

Sequence Variation in the tRNA Genes of Human Mitochondrial DNA

2005 ◽  
Vol 60 (5) ◽  
pp. 587-597 ◽  
Author(s):  
Tiina Vilmi ◽  
Jukka S. Moilanen ◽  
Saara Finnilä ◽  
Kari Majamaa
Keyword(s):  
Mitochondrial Dna ◽  
Sequence Variation ◽  
Trna Genes ◽  
Human Mitochondrial Dna
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